Trace elements play a critical role for microbial activity in anaerobic digestion (AD) but their effects were probably overestimated in batch tests and should be comparably evaluated in continuous systems. In this study, Fe2+, Co2+, Ni2+, Cu2+ and Zn2+ were added in different concentrations to manure wastewater, and the effects were compared in both batch and continuous systems. The results were used to demonstrate suitable trace element compositions for AD of dairy and swine wastewater, and to compare the outcomes from batch and continuous systems. Fe2+ and Zn2+ were identified as being the most efficient stimulant of dairy and swine wastewater respectively. The addition of 5 mg/L Fe2+ and 0.4 mg/L Zn2+ increased the batch specific methane yield by 62% and 126% for dairy and swine wastewater, respectively. Nevertheless, a lower increment of 2% and 21%, for dairy and swine wastewater was obtained in the 120-day continuously-fed experiments. The 16S rRNA gene sequencing results indicated a relationship between the methanogens population, specific methanogenic activities, propionate, and dissolved hydrogen. Conclusively, the addition of a low dosage of Fe2+ and Zn2+ is a feasible strategy to enhance the methanogenic metabolism of the AD of dairy and swine wastewater respectively.